Starting phenix.real_space_refine (version: dev) on Thu Dec 15 19:58:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x59_6704/12_2022/5x59_6704_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x59_6704/12_2022/5x59_6704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x59_6704/12_2022/5x59_6704.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x59_6704/12_2022/5x59_6704.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x59_6704/12_2022/5x59_6704_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x59_6704/12_2022/5x59_6704_trim.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 34": "OD1" <-> "OD2" Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 626": "NH1" <-> "NH2" Residue "A TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 306": "OD1" <-> "OD2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 444": "OD1" <-> "OD2" Residue "B TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B GLU 565": "OE1" <-> "OE2" Residue "B ASP 580": "OD1" <-> "OD2" Residue "B TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 626": "NH1" <-> "NH2" Residue "B TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 887": "NH1" <-> "NH2" Residue "B TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 306": "OD1" <-> "OD2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 444": "OD1" <-> "OD2" Residue "C TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C ASP 580": "OD1" <-> "OD2" Residue "C TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 626": "NH1" <-> "NH2" Residue "C TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 887": "NH1" <-> "NH2" Residue "C TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 26838 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 8993 Chain: "B" Number of atoms: 8806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 8993 Chain: "C" Number of atoms: 8806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 8993 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ASER A 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER A 51 " occ=0.54 residue: pdb=" N ASER B 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER B 51 " occ=0.54 residue: pdb=" N ASER C 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER C 51 " occ=0.54 Time building chain proxies: 26.24, per 1000 atoms: 0.98 Number of scatterers: 26838 At special positions: 0 Unit cell: (152.1, 166.4, 179.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 153 16.00 O 5247 8.00 N 4401 7.00 C 17037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.06 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.05 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.04 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.04 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.04 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.02 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.01 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.06 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.06 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.04 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.04 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.04 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.02 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.01 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.06 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.05 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.04 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.04 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.04 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.02 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.01 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM26570 O5 NAG B1401 .*. O " rejected from bonding due to valence issues. Atom "HETATM26710 O5 NAG C1401 .*. O " rejected from bonding due to valence issues. Atom "HETATM26430 O5 NAG A1401 .*. O " rejected from bonding due to valence issues. Atom "HETATM26822 O5 NAG C1409 .*. O " rejected from bonding due to valence issues. Atom "HETATM26542 O5 NAG A1409 .*. O " rejected from bonding due to valence issues. Atom "HETATM26682 O5 NAG B1409 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.07 Conformation dependent library (CDL) restraints added in 7.9 seconds 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6384 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 48 sheets defined 23.6% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 37 through 40 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.676A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 342 through 350 Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.195A pdb=" N LEU A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 390' Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 410 through 418 removed outlier: 3.613A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.547A pdb=" N SER A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 456 removed outlier: 5.043A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 814 through 823 Processing helix chain 'A' and resid 824 through 852 removed outlier: 3.639A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 897 Processing helix chain 'A' and resid 907 through 914 Processing helix chain 'A' and resid 940 through 959 removed outlier: 4.472A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 983 removed outlier: 3.973A pdb=" N VAL A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 993 removed outlier: 3.717A pdb=" N SER A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1011 Processing helix chain 'A' and resid 1018 through 1041 Processing helix chain 'A' and resid 1062 through 1107 Processing helix chain 'B' and resid 37 through 40 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.676A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 342 through 350 Processing helix chain 'B' and resid 385 through 390 removed outlier: 4.196A pdb=" N LEU B 389 " --> pdb=" O PHE B 385 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 390' Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 410 through 418 removed outlier: 3.613A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.547A pdb=" N SER B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 removed outlier: 5.043A pdb=" N SER B 454 " --> pdb=" O SER B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 814 through 823 Processing helix chain 'B' and resid 824 through 852 removed outlier: 3.638A pdb=" N CYS B 828 " --> pdb=" O TYR B 824 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 897 Processing helix chain 'B' and resid 907 through 914 Processing helix chain 'B' and resid 940 through 959 removed outlier: 4.471A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 983 removed outlier: 3.974A pdb=" N VAL B 983 " --> pdb=" O ARG B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 993 removed outlier: 3.718A pdb=" N SER B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1011 Processing helix chain 'B' and resid 1018 through 1041 Processing helix chain 'B' and resid 1062 through 1107 Processing helix chain 'C' and resid 37 through 40 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.677A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 342 through 350 Processing helix chain 'C' and resid 385 through 390 removed outlier: 4.196A pdb=" N LEU C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER C 390 " --> pdb=" O SER C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 390' Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 410 through 418 removed outlier: 3.612A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 removed outlier: 3.548A pdb=" N SER C 435 " --> pdb=" O ALA C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 456 removed outlier: 5.042A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 814 through 823 Processing helix chain 'C' and resid 824 through 852 removed outlier: 3.639A pdb=" N CYS C 828 " --> pdb=" O TYR C 824 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER C 829 " --> pdb=" O GLY C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 897 Processing helix chain 'C' and resid 907 through 914 Processing helix chain 'C' and resid 940 through 959 removed outlier: 4.472A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 983 removed outlier: 3.973A pdb=" N VAL C 983 " --> pdb=" O ARG C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 993 removed outlier: 3.717A pdb=" N SER C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1011 Processing helix chain 'C' and resid 1018 through 1041 Processing helix chain 'C' and resid 1062 through 1107 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.251A pdb=" N ASP A 34 " --> pdb=" O VAL A 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 75 removed outlier: 4.073A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.547A pdb=" N ALA A 282 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.160A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.509A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.858A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA8, first strand: chain 'A' and resid 360 through 361 Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 375 removed outlier: 5.878A pdb=" N VAL A 374 " --> pdb=" O SER A 607 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 400 through 404 removed outlier: 6.788A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 407 through 409 Processing sheet with id=AB3, first strand: chain 'A' and resid 513 through 515 removed outlier: 6.071A pdb=" N SER A 557 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS A 503 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 555 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG A 505 " --> pdb=" O TRP A 553 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP A 553 " --> pdb=" O ARG A 505 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 618 through 619 Processing sheet with id=AB5, first strand: chain 'A' and resid 779 through 782 removed outlier: 3.562A pdb=" N ILE A 782 " --> pdb=" O ILE A1147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 803 through 804 Processing sheet with id=AB7, first strand: chain 'A' and resid 1122 through 1124 Processing sheet with id=AB8, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.252A pdb=" N ASP B 34 " --> pdb=" O VAL B 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 75 removed outlier: 4.072A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.547A pdb=" N ALA B 282 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.160A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.509A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.858A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AC6, first strand: chain 'B' and resid 360 through 361 Processing sheet with id=AC7, first strand: chain 'B' and resid 374 through 375 removed outlier: 5.878A pdb=" N VAL B 374 " --> pdb=" O SER B 607 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 400 through 404 removed outlier: 6.788A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 407 through 409 Processing sheet with id=AD1, first strand: chain 'B' and resid 513 through 515 removed outlier: 6.071A pdb=" N SER B 557 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS B 503 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B 555 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG B 505 " --> pdb=" O TRP B 553 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP B 553 " --> pdb=" O ARG B 505 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 618 through 619 Processing sheet with id=AD3, first strand: chain 'B' and resid 779 through 782 removed outlier: 3.561A pdb=" N ILE B 782 " --> pdb=" O ILE B1147 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 803 through 804 Processing sheet with id=AD5, first strand: chain 'B' and resid 1122 through 1124 Processing sheet with id=AD6, first strand: chain 'C' and resid 33 through 35 removed outlier: 6.251A pdb=" N ASP C 34 " --> pdb=" O VAL C 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 68 through 75 removed outlier: 4.073A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.548A pdb=" N ALA C 282 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.159A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.509A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.858A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AE4, first strand: chain 'C' and resid 360 through 361 Processing sheet with id=AE5, first strand: chain 'C' and resid 374 through 375 removed outlier: 5.878A pdb=" N VAL C 374 " --> pdb=" O SER C 607 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 400 through 404 removed outlier: 6.789A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 407 through 409 Processing sheet with id=AE8, first strand: chain 'C' and resid 513 through 515 removed outlier: 6.071A pdb=" N SER C 557 " --> pdb=" O ASN C 501 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N CYS C 503 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL C 555 " --> pdb=" O CYS C 503 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG C 505 " --> pdb=" O TRP C 553 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TRP C 553 " --> pdb=" O ARG C 505 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 618 through 619 Processing sheet with id=AF1, first strand: chain 'C' and resid 779 through 782 removed outlier: 3.563A pdb=" N ILE C 782 " --> pdb=" O ILE C1147 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 803 through 804 Processing sheet with id=AF3, first strand: chain 'C' and resid 1122 through 1124 840 hydrogen bonds defined for protein. 2241 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.51 Time building geometry restraints manager: 11.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4490 1.32 - 1.45: 7986 1.45 - 1.58: 14761 1.58 - 1.71: 3 1.71 - 1.84: 201 Bond restraints: 27441 Sorted by residual: bond pdb=" C7 NAG C1403 " pdb=" N2 NAG C1403 " ideal model delta sigma weight residual 1.337 1.428 -0.091 1.10e-02 8.26e+03 6.81e+01 bond pdb=" C7 NAG B1407 " pdb=" N2 NAG B1407 " ideal model delta sigma weight residual 1.337 1.428 -0.091 1.10e-02 8.26e+03 6.79e+01 bond pdb=" C7 NAG B1403 " pdb=" N2 NAG B1403 " ideal model delta sigma weight residual 1.337 1.428 -0.091 1.10e-02 8.26e+03 6.78e+01 bond pdb=" C7 NAG A1407 " pdb=" N2 NAG A1407 " ideal model delta sigma weight residual 1.337 1.428 -0.091 1.10e-02 8.26e+03 6.78e+01 bond pdb=" C7 NAG A1403 " pdb=" N2 NAG A1403 " ideal model delta sigma weight residual 1.337 1.427 -0.090 1.10e-02 8.26e+03 6.74e+01 ... (remaining 27436 not shown) Histogram of bond angle deviations from ideal: 97.84 - 106.65: 933 106.65 - 115.46: 16108 115.46 - 124.27: 19493 124.27 - 133.07: 726 133.07 - 141.88: 54 Bond angle restraints: 37314 Sorted by residual: angle pdb=" N SER A 350 " pdb=" CA SER A 350 " pdb=" C SER A 350 " ideal model delta sigma weight residual 110.35 97.96 12.39 1.36e+00 5.41e-01 8.30e+01 angle pdb=" N SER C 350 " pdb=" CA SER C 350 " pdb=" C SER C 350 " ideal model delta sigma weight residual 110.35 97.96 12.39 1.36e+00 5.41e-01 8.30e+01 angle pdb=" N SER B 350 " pdb=" CA SER B 350 " pdb=" C SER B 350 " ideal model delta sigma weight residual 110.35 97.96 12.39 1.36e+00 5.41e-01 8.30e+01 angle pdb=" N ILE A 997 " pdb=" CA ILE A 997 " pdb=" C ILE A 997 " ideal model delta sigma weight residual 109.34 125.10 -15.76 2.08e+00 2.31e-01 5.74e+01 angle pdb=" N ILE C 997 " pdb=" CA ILE C 997 " pdb=" C ILE C 997 " ideal model delta sigma weight residual 109.34 125.10 -15.76 2.08e+00 2.31e-01 5.74e+01 ... (remaining 37309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.90: 15581 26.90 - 53.80: 582 53.80 - 80.71: 67 80.71 - 107.61: 12 107.61 - 134.51: 12 Dihedral angle restraints: 16254 sinusoidal: 6264 harmonic: 9990 Sorted by residual: dihedral pdb=" CA SER B 856 " pdb=" C SER B 856 " pdb=" N GLN B 857 " pdb=" CA GLN B 857 " ideal model delta harmonic sigma weight residual -180.00 -45.49 -134.51 0 5.00e+00 4.00e-02 7.24e+02 dihedral pdb=" CA SER C 856 " pdb=" C SER C 856 " pdb=" N GLN C 857 " pdb=" CA GLN C 857 " ideal model delta harmonic sigma weight residual -180.00 -45.50 -134.50 0 5.00e+00 4.00e-02 7.24e+02 dihedral pdb=" CA SER A 856 " pdb=" C SER A 856 " pdb=" N GLN A 857 " pdb=" CA GLN A 857 " ideal model delta harmonic sigma weight residual -180.00 -45.53 -134.47 0 5.00e+00 4.00e-02 7.23e+02 ... (remaining 16251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3415 0.089 - 0.177: 651 0.177 - 0.266: 140 0.266 - 0.355: 33 0.355 - 0.444: 12 Chirality restraints: 4251 Sorted by residual: chirality pdb=" CA ALA C1018 " pdb=" N ALA C1018 " pdb=" C ALA C1018 " pdb=" CB ALA C1018 " both_signs ideal model delta sigma weight residual False 2.48 2.04 0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CA ALA A1018 " pdb=" N ALA A1018 " pdb=" C ALA A1018 " pdb=" CB ALA A1018 " both_signs ideal model delta sigma weight residual False 2.48 2.04 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CA ALA B1018 " pdb=" N ALA B1018 " pdb=" C ALA B1018 " pdb=" CB ALA B1018 " both_signs ideal model delta sigma weight residual False 2.48 2.04 0.44 2.00e-01 2.50e+01 4.85e+00 ... (remaining 4248 not shown) Planarity restraints: 4779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 280 " -0.026 2.00e-02 2.50e+03 5.23e-02 2.74e+01 pdb=" CD GLN A 280 " 0.091 2.00e-02 2.50e+03 pdb=" OE1 GLN A 280 " -0.033 2.00e-02 2.50e+03 pdb=" NE2 GLN A 280 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 280 " -0.026 2.00e-02 2.50e+03 5.23e-02 2.74e+01 pdb=" CD GLN B 280 " 0.091 2.00e-02 2.50e+03 pdb=" OE1 GLN B 280 " -0.033 2.00e-02 2.50e+03 pdb=" NE2 GLN B 280 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 280 " -0.025 2.00e-02 2.50e+03 5.22e-02 2.72e+01 pdb=" CD GLN C 280 " 0.090 2.00e-02 2.50e+03 pdb=" OE1 GLN C 280 " -0.033 2.00e-02 2.50e+03 pdb=" NE2 GLN C 280 " -0.032 2.00e-02 2.50e+03 ... (remaining 4776 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 75 2.16 - 2.85: 9668 2.85 - 3.53: 36090 3.53 - 4.22: 66762 4.22 - 4.90: 109335 Nonbonded interactions: 221930 Sorted by model distance: nonbonded pdb=" OE1 GLN B 627 " pdb=" CG2 VAL C 271 " model vdw 1.477 3.460 nonbonded pdb=" OE1 GLN A 627 " pdb=" CG2 VAL B 271 " model vdw 1.498 3.460 nonbonded pdb=" OH TYR B 351 " pdb=" CE1 TYR B 361 " model vdw 1.507 3.340 nonbonded pdb=" OH TYR A 351 " pdb=" CE1 TYR A 361 " model vdw 1.507 3.340 nonbonded pdb=" OH TYR C 351 " pdb=" CE1 TYR C 361 " model vdw 1.508 3.340 ... (remaining 221925 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 50 or resid 52 through 1206 or resid 1401 throu \ gh 1410)) selection = (chain 'B' and (resid 18 through 50 or resid 52 through 1206 or resid 1401 throu \ gh 1410)) selection = (chain 'C' and (resid 18 through 50 or resid 52 through 1206 or resid 1401 throu \ gh 1410)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 153 5.16 5 C 17037 2.51 5 N 4401 2.21 5 O 5247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.250 Check model and map are aligned: 0.440 Convert atoms to be neutral: 0.250 Process input model: 86.030 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4107 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.141 27441 Z= 0.706 Angle : 1.645 25.582 37314 Z= 0.936 Chirality : 0.080 0.444 4251 Planarity : 0.009 0.114 4779 Dihedral : 14.813 134.510 9762 Min Nonbonded Distance : 1.477 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 1.33 % Allowed : 13.22 % Favored : 85.45 % Rotamer Outliers : 4.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.22 % Twisted Proline : 0.00 % Twisted General : 1.66 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.12), residues: 3390 helix: -3.00 (0.13), residues: 675 sheet: -1.20 (0.20), residues: 639 loop : -3.02 (0.11), residues: 2076 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 619 time to evaluate : 3.176 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 32 residues processed: 746 average time/residue: 0.3836 time to fit residues: 444.9793 Evaluate side-chains 391 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 359 time to evaluate : 2.953 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3158 time to fit residues: 21.1853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 3.9990 chunk 259 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 268 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 310 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS A 298 HIS A 599 GLN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN A 792 GLN A 812 ASN A 832 ASN A 842 GLN A 848 ASN A 870 ASN ** A 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 ASN A1176 ASN B 236 ASN B 346 GLN B 599 GLN ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN B 792 GLN B 800 GLN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 ASN B 832 ASN B 839 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 870 ASN ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1028 ASN B1072 ASN B1104 ASN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1163 ASN C 199 ASN ** C 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN C 800 GLN C 812 ASN C 832 ASN C 842 GLN C 870 ASN ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 GLN C1028 ASN C1104 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4520 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 27441 Z= 0.291 Angle : 1.102 21.902 37314 Z= 0.519 Chirality : 0.056 0.406 4251 Planarity : 0.007 0.111 4779 Dihedral : 9.212 106.806 3891 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.33 % Favored : 88.38 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 0.68 % Twisted General : 0.92 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.13), residues: 3390 helix: -1.36 (0.17), residues: 684 sheet: -0.83 (0.22), residues: 600 loop : -2.83 (0.12), residues: 2106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 423 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 40 residues processed: 479 average time/residue: 0.3614 time to fit residues: 278.6900 Evaluate side-chains 341 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 301 time to evaluate : 2.962 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2490 time to fit residues: 22.5522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 258 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 311 optimal weight: 0.9990 chunk 336 optimal weight: 5.9990 chunk 277 optimal weight: 0.0770 chunk 308 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 602 ASN ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 GLN ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN B 36 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN C 670 HIS C 733 GLN C 769 GLN C 832 ASN C1009 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5055 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 27441 Z= 0.304 Angle : 1.086 23.043 37314 Z= 0.503 Chirality : 0.054 0.300 4251 Planarity : 0.007 0.106 4779 Dihedral : 8.774 114.573 3891 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.13 % Favored : 86.57 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.68 % Twisted Proline : 1.36 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.13), residues: 3390 helix: -0.77 (0.18), residues: 702 sheet: -0.96 (0.20), residues: 687 loop : -2.59 (0.13), residues: 2001 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 360 time to evaluate : 3.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 20 residues processed: 407 average time/residue: 0.3676 time to fit residues: 241.1700 Evaluate side-chains 306 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 286 time to evaluate : 3.131 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 2 residues processed: 20 average time/residue: 0.2453 time to fit residues: 13.2826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 161 optimal weight: 30.0000 chunk 34 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 208 optimal weight: 8.9990 chunk 312 optimal weight: 0.7980 chunk 330 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 chunk 295 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN A 907 GLN A 988 GLN A1028 ASN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 HIS ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 819 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 ASN C 319 GLN C 501 ASN C1023 GLN ** C1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5151 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.099 27441 Z= 0.239 Angle : 1.007 21.289 37314 Z= 0.460 Chirality : 0.051 0.292 4251 Planarity : 0.006 0.107 4779 Dihedral : 8.332 111.485 3891 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.98 % Favored : 87.76 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.68 % Twisted Proline : 1.36 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.14), residues: 3390 helix: -0.30 (0.19), residues: 702 sheet: -0.47 (0.22), residues: 600 loop : -2.56 (0.12), residues: 2088 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 333 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 28 residues processed: 385 average time/residue: 0.3544 time to fit residues: 223.4623 Evaluate side-chains 309 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 281 time to evaluate : 2.970 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 2 residues processed: 28 average time/residue: 0.2615 time to fit residues: 17.4014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 275 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 246 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 282 optimal weight: 5.9990 chunk 228 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 168 optimal weight: 20.0000 chunk 296 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 785 ASN ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 GLN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN ** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 ASN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5376 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 27441 Z= 0.267 Angle : 1.022 21.484 37314 Z= 0.470 Chirality : 0.051 0.251 4251 Planarity : 0.006 0.111 4779 Dihedral : 8.307 112.892 3891 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.34 % Favored : 86.45 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.68 % Twisted Proline : 1.36 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.14), residues: 3390 helix: -0.05 (0.19), residues: 669 sheet: -0.52 (0.21), residues: 618 loop : -2.61 (0.13), residues: 2103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 336 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 23 residues processed: 366 average time/residue: 0.3636 time to fit residues: 216.5011 Evaluate side-chains 310 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 287 time to evaluate : 3.126 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 23 outliers final: 1 residues processed: 23 average time/residue: 0.2448 time to fit residues: 14.7418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 0.9990 chunk 297 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 194 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 330 optimal weight: 3.9990 chunk 274 optimal weight: 30.0000 chunk 153 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 681 HIS ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 GLN B 842 GLN B1009 GLN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1176 ASN C 91 HIS C 236 ASN C 800 GLN ** C 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5752 moved from start: 0.8646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 27441 Z= 0.395 Angle : 1.127 21.626 37314 Z= 0.530 Chirality : 0.056 0.305 4251 Planarity : 0.007 0.109 4779 Dihedral : 8.720 112.274 3891 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 24.43 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.52 % Favored : 86.04 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.68 % Twisted Proline : 0.68 % Twisted General : 0.64 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.13), residues: 3390 helix: -0.44 (0.19), residues: 666 sheet: -0.90 (0.21), residues: 624 loop : -2.80 (0.12), residues: 2100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 346 time to evaluate : 3.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 43 outliers final: 18 residues processed: 373 average time/residue: 0.3897 time to fit residues: 241.4978 Evaluate side-chains 290 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 272 time to evaluate : 3.135 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.2783 time to fit residues: 13.5849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 188 optimal weight: 0.1980 chunk 241 optimal weight: 10.0000 chunk 187 optimal weight: 0.4980 chunk 278 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 329 optimal weight: 0.7980 chunk 206 optimal weight: 0.1980 chunk 200 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 319 GLN ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN A1169 ASN ** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN B 280 GLN B 319 GLN B 501 ASN B1016 ASN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 ASN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 GLN C 785 ASN C 870 ASN C1201 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5595 moved from start: 0.8882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 27441 Z= 0.218 Angle : 1.006 20.078 37314 Z= 0.459 Chirality : 0.050 0.304 4251 Planarity : 0.006 0.118 4779 Dihedral : 8.186 111.005 3891 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.48 % Favored : 87.25 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.68 % Twisted Proline : 1.36 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.14), residues: 3390 helix: 0.00 (0.19), residues: 669 sheet: -0.89 (0.20), residues: 663 loop : -2.67 (0.13), residues: 2058 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 324 time to evaluate : 3.086 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 19 residues processed: 349 average time/residue: 0.3683 time to fit residues: 209.3555 Evaluate side-chains 301 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 282 time to evaluate : 2.878 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.2415 time to fit residues: 12.7732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 196 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 224 optimal weight: 0.7980 chunk 162 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 259 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 GLN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1169 ASN ** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 HIS C 107 GLN C 785 ASN C 870 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5715 moved from start: 0.9276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 27441 Z= 0.273 Angle : 1.019 20.680 37314 Z= 0.467 Chirality : 0.051 0.323 4251 Planarity : 0.006 0.116 4779 Dihedral : 8.204 111.183 3891 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.43 % Favored : 86.36 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.68 % Twisted Proline : 1.36 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.14), residues: 3390 helix: 0.00 (0.19), residues: 672 sheet: -0.78 (0.21), residues: 627 loop : -2.63 (0.13), residues: 2091 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 292 time to evaluate : 3.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 14 residues processed: 308 average time/residue: 0.3782 time to fit residues: 190.7534 Evaluate side-chains 277 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 263 time to evaluate : 3.129 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.2764 time to fit residues: 11.5428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 1.9990 chunk 315 optimal weight: 8.9990 chunk 288 optimal weight: 4.9990 chunk 307 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 chunk 133 optimal weight: 7.9990 chunk 241 optimal weight: 20.0000 chunk 94 optimal weight: 0.7980 chunk 277 optimal weight: 0.1980 chunk 290 optimal weight: 0.0970 chunk 306 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1169 ASN B 36 GLN B 167 HIS B 800 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 870 ASN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 ASN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5610 moved from start: 0.9504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 27441 Z= 0.214 Angle : 0.980 19.864 37314 Z= 0.447 Chirality : 0.049 0.272 4251 Planarity : 0.006 0.109 4779 Dihedral : 7.942 110.682 3891 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.39 % Favored : 87.34 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.68 % Twisted Proline : 1.36 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.14), residues: 3390 helix: 0.25 (0.20), residues: 675 sheet: -0.91 (0.21), residues: 663 loop : -2.58 (0.13), residues: 2052 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 305 time to evaluate : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 310 average time/residue: 0.3956 time to fit residues: 200.8685 Evaluate side-chains 282 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 274 time to evaluate : 3.299 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.2653 time to fit residues: 8.2883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 0.0030 chunk 324 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 225 optimal weight: 0.7980 chunk 340 optimal weight: 0.0570 chunk 313 optimal weight: 10.0000 chunk 271 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 overall best weight: 0.7310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 HIS ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 ASN B 870 ASN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 GLN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN C 842 GLN C 870 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5633 moved from start: 0.9701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 27441 Z= 0.217 Angle : 0.990 19.972 37314 Z= 0.450 Chirality : 0.049 0.286 4251 Planarity : 0.006 0.113 4779 Dihedral : 7.866 112.030 3891 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.98 % Favored : 86.78 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.68 % Twisted Proline : 1.36 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.14), residues: 3390 helix: 0.37 (0.20), residues: 666 sheet: -0.91 (0.21), residues: 663 loop : -2.55 (0.13), residues: 2061 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 290 time to evaluate : 3.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 295 average time/residue: 0.3709 time to fit residues: 181.2432 Evaluate side-chains 261 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 256 time to evaluate : 2.994 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2820 time to fit residues: 6.7887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 0.6980 chunk 289 optimal weight: 7.9990 chunk 83 optimal weight: 0.1980 chunk 250 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 271 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 279 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 870 ASN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 719 ASN C 800 GLN ** C 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 870 ASN C1023 GLN ** C1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.208651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.179552 restraints weight = 95975.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.180213 restraints weight = 135001.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.182692 restraints weight = 76472.397| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4576 r_free = 0.4576 target_work(ls_wunit_k1) = 0.209 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4576 r_free = 0.4576 target_work(ls_wunit_k1) = 0.209 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.9946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 27441 Z= 0.230 Angle : 0.981 19.873 37314 Z= 0.446 Chirality : 0.049 0.283 4251 Planarity : 0.006 0.111 4779 Dihedral : 7.839 112.193 3891 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.78 % Favored : 86.99 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.68 % Twisted Proline : 1.36 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.14), residues: 3390 helix: 0.40 (0.20), residues: 663 sheet: -0.88 (0.20), residues: 672 loop : -2.56 (0.13), residues: 2055 =============================================================================== Job complete usr+sys time: 5373.29 seconds wall clock time: 99 minutes 16.27 seconds (5956.27 seconds total)